We invite Lee Miller, Jiahua Guo, and Archana Dayalu to co-edit this page.

Running WRF (and/or WRF-Chem) on Harvard Odyssey: REAL cases

PART I. Setting up/Configuration/Compilation.

Instructions in this part assume you want to compile and run your own version of WRF. However, note that a compiled usable version of WRF/WRF-Chem v3.6.1 including all external utilities and supplementary geography datasets that you can copy to your preferred run directory is already located at:

/n/holylfs/INTERNAL_REPOS/CLIMATE_MODELS/WRF_CHEM_3-6-1

This folder (hereafter $CLIMATE_MODELS) contains the WRF-ARW model, the WRF Pre-processing system (WPS; used for real test cases), the chemistry module add-on, the complete WRF geography dataset (for use with WPS and WRF-Chem), and other utilities needed for WRF-Chem. Note: WPS, WRF-Chem not relevant for idealized cases.

Note 2: With the exception of the geography data set which is really big, copy the WRF_CHEM_3-6-1 folder to a location you are going to run it from. Soft link to the geography data set in the $CLIMATE_MODELS folder..

If you're going to be using WRF meteorology output to drive the STILT LPDM (http://stilt-model.org/index.php/Main/HomePage) you will need to make some changes to the Registry file before compiling. Some basic instructions for this are located in $CLIMATE_MODELS folder as a README_WRF-STILT_modifications.txt file.

unset MPI_LIB #unset for WPS, where WPS is used for real WRF simulations

### ...... For WRF-Chem: ...... ###

export WRF_EM_CORE=1

export WRF_NMM_CORE=0

export WRF_CHEM=1

Now, configure and compile. WRF must be compiled before WPS.

#(3) Configure WRF

./configure

#(4) Choose 15. (dmpar) to compile MPI version with Intel compilers

**Note! Do not use dm+sm or smpar options with WRF-Chem!! Choose either serial or dmpar**

#(5) Modify the file “configure.wrf” (around lines 149-150) to read the following. Note that you have to do this each time you run ./configure, because the configure.wrf script is overwritten each time.

DM_FC = mpiifort -f90=$(SFC)

DM_CC = mpiicc -cc=$(SCC) -DMPI2_SUPPORT

#(6) Compile WRF before WPS!! Compilation will take a while. If you're on an interactive shell, remove the "&" to avoid timing out.

# For real cases:

./compile em_real &> compile.log

#(7) Configure WPS

#Likely you will need GRIB2 Support...so Choose option #19:

#Linux x86_64, Intel compiler (dmpar)

./configure

#(8) Compile WPS

./compile &> compile.output

#(1)-(8) is adapted from Plamen's advice for v3.9.1

Now that the main WRF and WPS programs are compiled, it's time to think about utilities specific WRF-Chem. If you are planning on running WRF-Chem, you will additionally need to compile some utilities to make sure your chemical data is in the right format. Specifically, you will likely need to compile convert_emiss.exe; prep-chem-src, and mozbc. These are just examples; you may find that you may need additional ones.

If compilation was successful, you should see convert_emiss.exe in the WRFV3/chem folder.

#(10) Compile PREP-CHEM-SOURCES (available HERE), a mapping utility for converting raw anthropogenic chemical fields to binary intermediates that are then fed into convert_emiss.exe. Unzip the tar.gz file into your main WRF folder. There are some typos, and missing details in the pdf guide above, so a modified version of the instructions (and Paul Edmon's help rebuilding HDF5 to fix an error message) enabled successful compilation of the utility. The modified instructions are located here:

#(11) The anthro_emiss utility (ANTHRO). Like prep-chem, this is another (possibly less versatile) option for getting your anthropogenic chemical fields the wrf-chem format. It appears that it's useful for very specific data sets (like EDGAR-HTAP). But it also appears to be more straightforward to use, if you aren't rigid about your emissions inventory choice (i.e., if EDGAR-HTAP is sufficient for your purposes). If you want to set it up on your own, go here (https://www.acom.ucar.edu/wrf-chem/download.shtml) and click "anthro_emiss" at the bottom. Or you could use what is already downloaded and compiled (following the intstructions in the README):

/n/holylfs/INTERNAL_REPOS/CLIMATE_MODELS/WRF_CHEM_3-6-1/WRF/ANTHRO

#(12) The MOZBC utility for mapping chemical boundary conditions to your WRF-Chem domain has already been compiled and saved in the $CLIMATE_MODELS WRF-Chem folder, following the instructions in the README_mozbc file. You can use that, or if you wanted, download and compile MOZBC on your own. The initial files are based on MOZART 4-GEOS 5 output (6hr, 1.9x2.5deg, 56-level) datasets (https://www.acom.ucar.edu/wrf-chem/mozart.shtml). Read the README file for compilation instructions if you're doing this on your own; on odyssey you might have to do the following: export NETCDF_DIR=$NETCDF_HOME before compilation, and same with MEGAN instructions (#13 below). Otherwise you can use the compiled version located at:

/n/holylfs/INTERNAL_REPOS/CLIMATE_MODELS/WRF_CHEM_3-6-1/MOZBC

#(13) MEGAN bio emissions. A compiled version is located at the path below. (Read the README file for details if you want to compile your own version. Make sure your NETCDF_DIR variable is set if so, and make sure your make_util file is executable. Then run ./make_util megan_bio_emiss). Make sure you also have the input data you need from https://www.acom.ucar.edu/wrf-chem/download.shtml . Scroll to the bottom "For bio_emiss input files only" and fill out the requested spatiotemporal information. Then select "bio_emiss input files".

PART II. Running WPS and WRF: Overview/General Steps

Now that you have a compiled version of WRF and WPS, you are ready to set up your model runs. Since these are for real cases, you need access to initialization data sets. You will need to figure out the initialization data set best suited to your domain and purposes. For the examples for China provided here, we are using GRIB2 NCEP FNL Operational Model Global Tropospheric Analyses, continuing from July 1999 (http://dx.doi.org/10.5065/D6M043C6). For these examples, the files are already downloaded. Instructions to link to them are noted where necessary.

Regardless of whether you are running WRF or WRF-Chem, it is important that you do the following first and in this order (detailed instructions follow, including in the examples in Part III and IV):

(1) Run WPS (geogrid.exe, ungrib.exe, metgrid.exe) to create real data-based initialization files with of form met_em.d0X.YYYY-MM-DD_hh:mm:ss.nc

(2) Run real.exe to generate input and boundary files of form wrfinput_d0*, wrfbdy_d01 (and optionally wrffdda_d0*) to initialize WRF model

If you are running WRF without chemistry, you can go ahead and run the main WRF model at this point. If you are running WRF-Chem, this is the point at which you run your chemistry data prep program (i.e., prep-chem-src, anthro_emis, and/or convert_emiss) which requires wrfinput_d0* files to actually work. Once you have your correctly formatted chemical data (they should be in the form wrfchemi_00z_d01 and wrfchemi_12z_d01). Once you are done with this and have all your requisite chem data in the right format stored or linked in the WRFV3/test/em_real folder, you can run the wrf.exe model.

Step 1: Running WPS (WRF Pre-processing System)

The pre-processing to create a real data-based initialization file.Read the README file in the parent WPS folder for a quick guide on what the programs do.

#note: be aware of 90-day retention policy of scratch data. Make sure you've emptied any files from previous runs in the dump dirs.

3. link Vtable (it's like a Rosetta Stone) to appropriate GRIB data type to prepare for ungribbing. e.g., for GFS data. WRF has a bunch of Vtables already in the Variable_Table subfolder of ungrib, but sometimes you will need to do some sleuthing and download the one that you actually need into the Variable_Tables folder. For the examples that follow, this is exactly what we'll need to do.

ln -sf ungrib/Variable_Tables/Vtable.theVtableYouWantToUse Vtable

4. link the GRIB data that you are going to use

./link_grib.csh /your_GRIB_data_path/XXX*

#This should update GRIBFILE.AAA, .AAB, etc links in pwd.

5. Run ungrib

mpirun -np 1 ./ungrib.exe >& ungrib.output

#You should see FILE:YYYY-MM-DD_hh in your folder prescribed by “prefix”

3. Examine the run_real.log file. You should see SUCCESS EM_REAL INIT printed at the end.

4. Make sure you have the following files output from this step:

wrfinput_d0* (one for each domain)

wrfbdy_d01 (just for d01)

wrffdda_d01 (just for d01 since nudging is happening only in this domain)

This is the point at which you have some separate additional steps (in red font, below) if you are running WRF-Chem. This is because successfully running these utilities for your simulation domain(s) requires the wrfinput (and wrfbdy, if using mozbc) files from real.exe. If you are not running WRF-Chem, skip this subsection and continue with Step 10 below.

6. Make sure your binary emissions files are saved in WRFV3/test/em_real either as hard or soft links. They MUST be in this directory in some form.

7. Turn your chemistry back on (chem_opt=XXX) in the namelist.wrf file.

8. Run convert_emiss.exe to convert the chemistry data from binary intermediate to WRF input form

9. You should have your relevant chem data in WRFV3/test/em_real at this point, ready for ingestion by the wrf model. At this point, the key files input files that WRF-Chem expects in order to run successfully may now include, but is not limited, to the following:

wrfbiochemi_<domain> #if you planned to include biogenic chem

wrfchemi_00z_<domain> #if you planned to use anthropogenic chem, for two sets of time 00z and 12z

wrfchemi_12z_<domain>

wrfbdy_d01 #Boundary file, should include chemical boundary conditions from mozbc for example if you chose to go that route.

wrfinput_<domain> #your standard initialization file from real.exe

wrffdda_<domain> #for the domain that you're nudging in (if you are nudging).

10. If everything looks in order, run the wrf model. This is the only step that has significant benefit from running in parallel!

sbatch run_wrf.sh #Edit this script as needed; a template is provided.

11. You should now have netcdf files of format, stored in /n/your_scratch_dir_path/WRFOUT/. If you are planning to drive an LPDM like STILT with these met files, these need to eventually be converted to .arl format using WRF2ARL directory contents. This is something that will be treated in a separate page. It is highly recommended that you get familiar with NCL (and have access to ncview) for post-processing and visualization of the wrfout files.

wrfout_d0#_YYYY-MM-DD_hh:mm:ss

PART III. Running WRF With Chemistry: A PM2.5 example

The purpose of this example is to take the general steps listed above and actually run a three nested domain WRF-Chem PM2.5 simulation over Beijing during the January 2013 severe haze event and compare with observations. We are going to run WRF-Chem for a total of 10 days from Jan 6 2013 00:00UTC to Jan 16 2013 00:00UTC. We establish 5 days for model spin-up such that the usable simulation time period is 5 days. Make sure you have a local copy of the /n/holylfs/INTERNAL_REPOS/CLIMATE_MODELS/WRF_CHEM_3-6-1/WRF directory and contents. You don't need to copy the geography data set.

Thanks to Meng Gao at Harvard China Project and Thomas Lauvaux at PSU for help with this and for providing their WRF-Chem namelist templates for this example!

NOTE: Running "plain wrf" without chemistry is everything below except you would ignore steps 3 through 6. If you're not interested in WRF-Chem, and wanted to do a plain WRF tutorial there are much better ones online, or you could just follow along here and skip steps 3 to 6.

At the end of this example you will have learned how to:

Get in the habit of using ncview for sanity-check visuals

Use the dust map from the WPS high-res geographical data set (namelist.input dust_opt=3), although this is less important for this winter exercise.

Use prep-chem-sources and convert_emis to format a gridded anthropogenic PM2.5 emissions file to the WRF forecast domain

Step 0.1.

At any point where you want to check the contents of a netcdf file as a sanity-check use ncview! This is an excellent habit to develop. Just type

ncview your_file.nc

and navigate through the variables and panes and make sure things look realistic.

Step 0.2

For wrf-chem, it's good practice to create a folder for use with various external utilities that you link your intermediate wrf files to. This will become clearer, but for now make sure you have a directory in your $CLIMATE_MODELS location that's entitled "UTILINP".

Step 1. Run WPS

Navigate to the WRF/WPS folder.

First customize the WPS namelist.wps file such that it looks like the following. Note that with the exception of the geog_data_path, all path variables should point to a writable dump directory of your choice. It is recommended you write to regal or a similar scratch space you have access to; the dump files take up space and aren't needed again after the run so they don't have to be stored in a permanent location. Consult the WRF user guide for detailed explanation of the namelist variables.

And you should see something like below. Once this is done, navigate to your geogrid dump folder that you specified in your namelist.wps file and visualize the three geo_em.<domain>.nc files using ncview. Make sure things look reasonable.

Now get ready to run ungrib. Since we will be using NCEP fnl data (GRIB2 format) for this run, we do some sleuthing to confirm the correct Vtable to use. Following the discussion here we download the appropriate Vtable separately (this one isn't included with the standard set of Vtables in WRFv3.6.1 because they recently updated the dataset). Note: I have already downloaded it and saved it: ungrib/Variable_Tables/Vtable.GFS_new

Copy namelist.input_pm25Beijing to namelist.input. Take a look at the namelist and confirm the dates and domain match your wps namelist

Make sure to turn off chemistry (chem_opt = 0) for this step.

Change the filepath in history_outname to reflect where you want your wrfchem output files to be saved.

Link the metgrid files to the test/em_real directory and make sure the namelist num_metgrid_levels and num_metgrid_soil_levels match what's in the metgrid files.

ln -s /n/your_scratch_dir_path/METEM_FILEDUMP/met_em* .

Run real.exe to output the necessary intermediate files for chem data processing. Check that the tail of the file says SUCCESS COMPLETE REAL_EM INIT

mpirun -np 1 ./real.exe >& run_real.log

You should have five files that real.exe produced. These currently only contain meteorological info, which is fine for running plain WRF-ARW. But – since we are running WRF-Chem – we need to run the additional utilities that either use the info contained in these files to map chemical data correctly (e.g., prep-chem-src) or modify the contents directly (e.g., mozbc for inputs of chemical boundary conditions into wrfbdy_d01).

wrfbdy_d01 #the outermost domain parameter boundary condition file

wrffdda_d01 #nudging file, we requested nudging in the outer domain

wrfinput_d<domain> #initial condition files for each of your study domains.

Create soft links of all the met_em.<domain>, wrfinput_<domain>, wrfbd_d01 files in your UTILINP folder. These will be used by the external utilities in the next steps.

Step 3. Generate your bio emissions using MEGAN

You will need access to the relevant MEGAN initial files, from https://www.acom.ucar.edu/wrf-chem/download.shtml

Make sure you are still using an interactive shell ('srun -n 1 --mem=10000 --pty --x11=first -p test -t 200 bash' should be sufficient). Navigate to the MEGAN directory in the $CLIMATE_MODELS directory (or wherever you have saved your local copy of everything)

Create a new text file called megan_bio_emiss.inp. This is your MEGAN namelist file.Note that as the README instructs, the leaf area index (lai) months requires the simulation month and the previous month such that for January (as our example here is) we have to simulate all months. Following the instructions in the README, you should populate to look like follows ... with the paths obviously reflecting where your WRF + external utility directories are located.

&control

domains = 3

start_lai_month = 1

end_lai_month = 12

wrf_dir = '/n/holylfs/LABS/kuang_lab/adayalu/WRF/UTILINP'

megan_dir = '/n/holylfs/LABS/kuang_lab/adayalu/WRF/MEGAN'

You should be ready to run the MEGAN bio emission utility

./megan_bio_emiss < megan_bio_emiss.inp > megan_bio_emiss.out

If the program ran correctly, you should get no messages and you should see three files in your MEGAN folder. Check them out with ncview.

Now that you have your bio emissions, it's time to get your anthropogenic emissions in the right format. We're going to use the EDGAR-HTAP PM2.5 emissions on a 0.1x0.1 deg annual global grid.

This option has been successfully tested if you're using EDGAR-HTAP emissions or IPCC emissions (for use with CAM-Chem) and seems a little less complicated than prep-chem-sources. In these examples, we will go this route. If you are starting with other emissions, you probably need to go the prep-chem route. I haven't spent much time figuring out how to use it; the anthro_emis option seemed most straightforward for now because I already had some familiarity with utilities in the same family (MEGAN, MOZBC).

Navigate to your ANTHRO folder

cd src

Link the EDGAR_HTAP_emi_PM2.5_2010.0.1x0.1.nc file from the anthro_data/MOZCART folder to this folder

Create a new text file called anthro_emis.inp. This will be your namelist file. Check out the README file for detailed instructions. Your namelist file should look like the following. This is constructed based on a hybrid of following instructions in the README file and the input file located in the anthro_data/EDGAR-HTAP/INP-Examples folder. Make sure you understand the purpose of the entries.

&CONTROL

anthro_dir = '/n/holylfs/LABS/kuang_lab/adayalu/WRF/ANTHRO/src'

domains = 3

wrf_dir = '/n/holylfs/LABS/kuang_lab/adayalu/WRF/UTILINP'

src_file_prefix = 'EDGAR_HTAP_emi_'

src_file_suffix = '_2010.0.1x0.1.nc'

src_names = 'PM2.5(1)'

sub_categories = 'emis_tot'

serial_output = .false.

start_output_time = '2010-12-01_00:00:00'

emissions_zdim_stag = 1

emis_map = 'PM_25(a)->PM2.5',

/

Note that the src_file_prefix and src_file suffix are concatenated with whatever is specified in src_names (here, PM2.5) to generate the full filename string.

Now run anthro_emis.

./anthro_emis < anthro_emis.inp > anthro_emis.out

and you should see six new files in the ANTHRO/src directory, one for each of the three domains. Check out the contents with ncview.

Use this utility if you're using something other than EDGAR-HTAP or things not listed in the anthro_emis README/instructions. In theory, anthro_emis could work for other emissions fields, but they have just not been tested.

Now that you have your bio emissions, it's time to get your anthropogenic emissions in the right format. Navigate to your PREP-CHEM-SRC-1.5 folder.

cd bin

Edit the prep_chem_sources.inp namelist file. Check out the README file for detailed instructions.

Step 5. Run real.exe again, with chem_opt turned on

Navigate to your WRFV3/test/em_real/ directory

Link your bio and anthro files to your WRFV3/test/em_real/ directory.

Open up the the namelist.input file and turn chem_opt back on (set it to 10).

Make sure kemit=1 (vertical levels in anthro emissions files...in this case it is 1...surface data).

Call up an interactive shell if you don't have one running. Run real.exe again. This incorporates the chem variables into the initial and boundary condition files so that MOZBC can populate them.

mpirun -np 1 ./real.exe > run_real.log

Check that the tail of the rsl.error.0000 file says "SUCCESS COMPLETE REAL_EM INIT"

This step modifies the wrf initial and boundary condition files that now have space for chemical data (since we re-ran real.exe with chem_opt on and anthro/bio fields)

Go to https://www.acom.ucar.edu/wrf-chem/mozart.shtml and submit a data request. This can take some time to process depending on your domain size request. Submit your bounding box, and times. For this exercise you can use what was already downloaded. This is available in the mozbc directory in the $CLIMATE_MODELS folder as a mozart4geos5-ZZZZ.nc file.

Navigate to your mozbc folder from the $CLIMATE_MODELS folder.

cd MOZBC

Recall the MOZBC utility is used to modify the wrfinput/wrfbdy files to contain chemical boundary conditions.

From the namelist.input file for this exercise in WRFV3/test/em_real, we see that chem_opt = 10. Referring to the WRF-Chem user manual for more details. This chemistry option uses the CBMZ chemical mechanism and MOSAIC using 8 sectional aerosol bins. We match this with what MOZBC provides as sample namelists and we pick CBMZ-MOSAIC_8bins.inp as our mozbc namelist file. Copy this to a new file and edit the new file as follows

cp CBMZ-MOSAIC_8bins.inp mozbc.inp

Now edit this file.

do_bc = .true.

do_ic = .true.

domain = 3

#FYI, I've found mozbc can be unhappy when the set directory path is too long.

dir_wrf = '/n/holylfs/LABS/kuang_lab/adayalu/WRF/UTILINP/' #obviously this should be your specific path.

dir_moz = '/n/holylfs/LABS/kuang_lab/adayalu/WRF/MOZBC/' #obviously this should be your specific path.

# fn_moz should look something like 'ha0004.nc'. #you will have to rename your mozart4geos5-ZZZZ.nc file whatever this is.

#In the species map (spc_map) section, delete the entry 'op2 -> C2H5OOH'. This isn't in the mozart4geos5 file, and leads to an error if it remains in there.

#(This knowledge is from trial and error.)

Exit editor.

ln -s mozart4geos5-ZZZZ.nc ha0004.nc #copy as link to "rename"

You are now ready to run mozbc. In your mozbc directory type:

./mozbc < mozbc.inp > mozbc.out

#tail mozbc.out should have a final line that reads:

bc_wrfchem completed successfully

Step 7. You're (FINALLY) ready to run WRF-Chem

Navigate back to your WRFV3/test/em_real directory. Check that you have the preferred path set to your WRFOUT directory (recommend regal or some scratch space with a lot of space) in your history_outname field. If you change the filename, note the only part of the filename that you should mess with is the part before '_d<domain>_d<date>'!

I liked to keep my frames hourly (a file is written out every simulation hour. More helpful with debugging if run fails. Up to you.)

Open up the script run_wrf.sh and make sure it looks ok.

Submit your wrf job

sbatch run_wrf.sh

squeue -u username #monitor your job status

If your run is successful you should start to see files populating your outpath:

With 15 cores on one node (using huce_amd queue) it took about 40 hours for this run to complete:

sacct -j 49862718 --format=JobID,JobName,MaxRSS,Elapsed

JobID JobName MaxRSS Elapsed

------------ ---------- ---------- ----------

49862718 wrfchem_t+ 1-15:32:54

49862718.ba+ batch 11588K 1-15:32:54

Step 8. Post-Processing and data visualization

I primarily use NCL, and/or some combination of NCL and R. Pick whatever you're used to for processing netcdf files. If you're going to use NCL, I recommend looking at the very well documented examples on their website. For example, start with the one about how to open and read netcdf files and go from there:

If you use ncview, you can quickly get a sense of how your simulation worked. Take a look at the PM2.5_DRY variable (3D Vars). You will notice that while the run completed successfully from a technical standpoint, it's actually way off. The PM2.5 values are unrealistic – two orders of magnitude lower than observations in the d03 domain – and this is most likely due to some combination of the following:

Accounting only for primary PM2.5. There is obviously all the secondary PM2.5 that needs the appropriate precursor species mapped as well. (25% to nearly 40% of PM2.5 in many cities in the region is secondary inorganic.)

My failure to process files correctly. While the wrfchemi, wrfbiochemi, and mozbc utilities seem to have gone through, it may not have done so correctly based on an inappropriate namelist parameter selection. For some reason, the surface emissions are not being read in correctly. We used EDGAR-HTAP from 2010 processed using the anthro_emis utility. In the past I have run a test of this using a more specialized inventory from 2010 pre-processed using NCL which led to a far more realistic PM2.5 simulation (i.e., surface emissions data was being read in).

inappropriate choices in the WRF-Chem namelist.input file.

In any case, this exercise should at least get you familiarity with the process of running WRF-Chem and set you up for being able to do second-order troubleshooting (like the more important question of why these values are unrealistic!).